Weight painting / vertex groups questions
You should follow some tutorials on rigging, like Darrin Lile's or Sebastian Lague's, it's better to first learn from scratch in my opinion.
Before parenting it's always better to make sure that the transforms (scale, rotation) have been applied, and that the normals of your mesh are correctly flipped.
For the vertex groups, when you'll parent the mesh to the armature With Automatic Weight, it will automatically create as many groups as you have bones, and the groups will have the names of the bones that control them. If the mesh already has some vertex groups from previous operations, it will keep them as long as their names are different but it won't interact with the parenting, so you should not have to care about that but you can always delete them if you prefer.
If you parent With Empty Groups, it will create as many groups as you have bones, but it won't affect any vertex to these groups, you'll need to do it either with the Assign button or in Weight Paint mode, this is the best method when you parent non organic objects like machine, robot, etc. as it let you define what part is supposed to be controlled by which bone and doesn't create any gradient influence.
For the armature, you can use the ones you currently have, except it seems incomplete, you should have a root bone, your lower legs or lower arms should have IK constraints, you should have the targets and pole targets for these constraints (you already have targets for your legs though), and make sure that these bones (root, targets, pole targets) have their Deform options disabled (which is not the case for your leg targets).